If you're setting this up as a pre-index script, then it would work the same for both scanned or swept documents, with the caveat that all of these batches are being routed to manual indexing (that is, they aren't skipping indexing because they were scanned/swept in full-index mode). As a user starts to index a batch, the hooked pre-index script is fired once for each document right at the beginning of the index operation for that document. So the script as you have it above is getting the keyword panel object and asking it to set the keyword value into the panel (not directly onto the document, just the keyword panel as the user sees it during indexing - the keyword value would be applied to the document when the user hits the index button). But - your script isn't setting a document type into the panel, so unless the documents coming into the index process already have a document type *and* that document type includes the "Project #/Cost Center" keyword type, you wouldn't see any result (because the script is trying to set a keyword value that isn't currently in the keyword panel). If this is the case (i.e. either the documents to be indexed don't have a document type, or they do but that document type doesn't include that keyword type) then you may need to modify this script to also set a document type into the panel before adding the keyword value.
